I can confirm that Wind Waker North American Version works with Dios Mios. I haven't had any issues with it. It works just as it would if I had the actual disc in it. I would say that the issue with the loading time would be your USB's fault, but you haven't had this issue with any other games. However, I haven't tested Wind Waker specifically with DM 2.9 and USB Loader GX rev. 1213. I've only tested Super Mario Sunshine with that.

I will try to run Wind Waker on my Wii with the same loader and DM version that you have and see if I get any long loading screens.

EDIT:

Okay, I tested Wind Waker with the same Loader and DM version you are using and get no errors. This leads me to conclude that if you followed the guide correctly, you have a bad rip or the issue is with your USB.

That list contains thumb drives and what not (in the 100gb and under category). Perhaps what you were using were USB1.1 devices? That certainly would be a cause and not worth submitting to the list (it's for USB 2.0 or 2.0/3.0 devices).

I have been trying to play my back up game cube games with configurable usb loader version 51 and dios mios 2.9. While wii games work, game cube games have not worked. When I try to start a game it gets stuck on the dios mios splash screen ( the screen with the gamecube logo and "dios Mios.") It just stays on that screen or eventually goes black. Occasionally it doesn't even go to that screen and just stays black. I have tried five or six games and have tried installing them with dm toolbox and burning them through configurable usb loader. I have a memory card and game disk in the system. The hard drive is a buffalo MiniStation Stealth and is formatted to active fat32. Sorry if this is confusing as I am writing this very late at night. Please help.

Hey. I've come up with a little issue using DIOS MIOS. Whenever I launch a game with a loader, during the DIOS MIOS splash screen a thick black border appears on the left side. Basically the screen moves horizontally to the right. It looks like this (http://i.imgur.com/4ADCd2G.png) in the game. You can see the screen as a whole but can clearly tell it's not in the center of the tv screen.

I've been using Wiiflow all the time but tried with USBLoader GX and the same happened so I think it's not about the loader. I encountered the same problem earlier but fixed it by reinstalling DM 2.8 with IOS236 using WAD Manager 1.7. All my previous installs were using MMM. But now I've tried to install various DM revisions with different IOSes and it doesn't get fixed.